Brucella thiophenivorans (DSM 7216, CCM 7492, CCUG 55412)

Name: Brucella thiophenivorans (DSM 7216, CCM 7492, CCUG 55412)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1895

Type strain

Strain Designation AK220

Culture col. no. DSM 7216 CCM 7492 CCUG 55412 AK220

NCBI tax ID(s) 571255

Special Collections DSMZ CCUG Literature strains

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Brucella thiophenivorans AK220 is a mesophilic, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from waste water.

Gram-negative rod-shaped colony-forming mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 48387

DSM 7216,CCM 7492,CCUG 55412

@ref 20215

Last LPSN update 2025-12-16 09:47:12

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Brucellaceae

Genus Brucella

Species Brucella thiophenivorans

Full scientific name Brucella thiophenivorans (Kämpfer et al. 2008) Hördt et al. 2020

Synonyms (1)

Ochrobactrum thiophenivorans

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
23342	negative	2 µm	rod-shaped
125438	negative			99
125439	negative			99.9

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period
23342	2 mm	beige, translucent	circular	1 day

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3055	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
3055	MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461) Composition: Na2HPO4 x 2 H2O 1.44135 g/l MgSO4 x 7 H2O 0.497018 g/l NH4Cl 0.298211 g/l KH2PO4 0.248509 g/l NaCl 0.0497018 g/l MnSO4 0.00994036 g/l CaCl2 0.00994036 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l Thiamine-HCl x 2 H2O 0.000248509 g/l p-Aminobenzoic acid 0.000248509 g/l Vitamin B12 0.000248509 g/l Pantothenic acid 0.000248509 g/l Riboflavin 0.000248509 g/l alpha-lipoic acid 0.000248509 g/l CoCl2 x 6 H2O 0.000188867 g/l Nicotine amide 0.000124254 g/l Nicotinic acid 0.000124254 g/l Folic acid 9.94036e-05 g/l Biotin 9.94036e-05 g/l MnCl2 x 4 H2O 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l Pyridoxamine hydrochloride 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l H3BO3 5.96421e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Distilled water
23342	MacConkey
23342	Nutrient agar (NA)
23342	PYE agar
23342	Reasoner's 2A agar (R2A)
23342	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3055	positive	growth	30	mesophilic
23342	positive	growth	25-30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
23342
125439		99.6

Compound production

3055

Compoundthiophene-2-carboxylate CoA esterase

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23342	37054 ChEBI	3-hydroxybutyrate	+	assimilation
23342	17879 ChEBI	4-hydroxybenzoate	-	assimilation
23342	16958 ChEBI	beta-alanine	+	assimilation
23342	17057 ChEBI	cellobiose	-	assimilation
23342	16383 ChEBI	cis-aconitate	-	assimilation
23342	16947 ChEBI	citrate	-	assimilation
23342	15824 ChEBI	D-fructose	+	assimilation
23342	8391 ChEBI	D-gluconate	+	assimilation
23342	17924 ChEBI	D-sorbitol	+	assimilation
23342	16865 ChEBI	gamma-aminobutyric acid	+	assimilation
23342		gamma-L-glutamate-4-nitroanilide	-	hydrolysis
23342	29991 ChEBI	L-aspartate	+	assimilation
23342	15971 ChEBI	L-histidine	-	assimilation
23342	15603 ChEBI	L-leucine	-	assimilation
23342		L-proline-4-nitroanilide	+	hydrolysis
23342	62345 ChEBI	L-rhamnose	-	assimilation
23342	68428 ChEBI	maltitol	-	assimilation
23342	17306 ChEBI	maltose	-	assimilation
23342	17268 ChEBI	myo-inositol	+	assimilation
23342	28037 ChEBI	N-acetylgalactosamine	+	assimilation
23342	506227 ChEBI	N-acetylglucosamine	+/-	assimilation
23342	91050 ChEBI	p-nitrophenyl phenyl phosphonate	+/-	hydrolysis
23342	15963 ChEBI	ribitol	-	assimilation
23342	9300 ChEBI	suberic acid	-	assimilation
23342	17992 ChEBI	sucrose	-	assimilation
23342	15708 ChEBI	trans-aconitate	-	assimilation
23342	27082 ChEBI	trehalose	-	assimilation

Enzymes

@ref	Value	Activity	Ec
23342	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	ketogluconate metabolism	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	allantoin degradation	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	threonine metabolism	100	10 of 10
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	propanol degradation	100	7 of 7
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	lipoate biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	CMP-KDO biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	vitamin B6 metabolism	72.73	8 of 11
66794	oxidative phosphorylation	72.53	66 of 91
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	lysine metabolism	69.05	29 of 42
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	pyrimidine metabolism	64.44	29 of 45
66794	tryptophan metabolism	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	glutathione metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	sulfopterin metabolism	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	isoprenoid biosynthesis	50	13 of 26
66794	ascorbate metabolism	50	11 of 22
66794	ethanol fermentation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	gallate degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	glycogen biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phenylpropanoid biosynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Wastewater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
3055	waste water	Göttingen	Germany	DEU	Europe
60578	Waste water		Germany	DEU	Europe	2000

Taxonmaps

69479

Global distribution of 16S sequence AM490617 (>99% sequence identity) for Ochrobactrum from Microbeatlas

Aquatic Samples	61
Soil Samples	35
Animal Samples	183
Plant Samples	31
Total Samples	310

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3055	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM225244v1 assembly for Brucella thiophenivorans DSM 7216	contig	GCA_002252445	571255.8	2854902268	571255	52.54
124043	ASM4193002v1 assembly for Brucella thiophenivorans DSM 7216	scaffold	GCA_041930025			571255	30.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3055	Ochrobactrum thiophenivorans partial 16S rRNA gene, type strain DSM 7216	AM490617	1387		571255

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Brucella thiophenivorans DSM 7216
NCBI: GCA_002252445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	81.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ochrobactrum thiophenivorans strain DSM 7216
PATRIC: 571255.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	95.49	no
125438	spore-forming	spore-formingⓘ	no	85.92	no
125438	aerobic	aerobicⓘ	yes	80.54	no
125438	thermophilic	thermophileⓘ	no	98.46	no
125438	flagellated	motile2+ⓘ	yes	53.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Deciphering the biodesulfurization potential of two novel Rhodococcus isolates from a unique Greek environment.	Glekas PD, Martzoukou O, Mastrodima ME, Zarkadoulas E, Kanakoglou DS, Kekos D, Pachnos M, Mavridis G, Mamma D, Hatzinikolaou DG.	AIMS Microbiol	10.3934/microbiol.2022032	2022
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment.	Kampfer P, Sessitsch A, Schloter M, Huber B, Busse HJ, Scholz HC	Int J Syst Evol Microbiol	10.1099/ijs.0.65407-0	2008

References

#3055	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7216
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#23342	Peter Kämpfer, Angela Sessitsch, Michael Schloter, Birgit Huber,Hans-Jürgen Busse, Holger C. Scholz: Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. IJSEM 58: 1426 - 1431 2008 ( DOI 10.1099/ijs.0.65407-0 , PubMed 18523190 )
#60578	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55412
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Brucella thiophenivorans (DSM 7216, CCM 7492, CCUG 55412)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002252445

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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